Genes coding for β-agarases and their use for producing agar biodegradation enzymes

ABSTRACT

The invention relates to the novel  Cytophaga drobachiensis  strain deposited in the DSMZ Collection (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures)) on May 8, 1998 under the number DSM 12170, the agaA gene coding for a β-agarase and having SEQ ID No. 1, the agaB gene coding for a β-agarase and having SEQ ID No. 3, said genes coding for a β-agarase of  Cytophaga drobachiensis  DSM 12170, and the specific nucleic acid sequence of the agaA gene coding for a specific peptide fragment AgaA′ which has conserved β-agarase activity, and having SEQ ID No. 5, as well as the protein AgaA of  C. drobachiensis  DSM 12170 having SEQ ID No. 2, the protein AgaB of  C. drobachiensis  DSM 12170 having SEQ ID No. 4 and said peptide fragment AgaA′ of  C. drobachiensis  DSM 12170 having SEQ ID No. 6.

The present invention relates to two novel genes coding for β-agarases and to their use for producing agar biodegradation enzymes.

It further relates to the Cytophaga drobachiensis strain from which these genes were isolated.

The sulfated galactans of Rhodophyceae, such as agars and carrageenans, represent the major polysaccharides of Rhodophyceae and are very widely used as gelling agents or thickeners in various branches of activity, especially the agri-foodstuffs sector. Approximately 6000 tonnes of agars and 22,000 tonnes of carrageenans are extracted annually from marine red algae for this purpose. Agars are produced industrially from red algae of the genera Gelidium and Gracilaria. Carrageenans are widely extracted from the genera Chondrus, Gigartina and Euchema.

Agaro-colloids are polysaccharide complexes consisting mainly of agars and agaroids. Each agaro-colloid has a different content of each of the above compounds, so its gelling strength is different. Agar gel comprises a matrix of double-helix polymer chains held together by hydrogen bonds.

There are two types of enzyme capable of degrading agars: α-agarases and β-agarases. β-Agarases act on the β-1,4 linkage and α-agarases act on the α-1,3 linkage.

Microorganisms which produce enzymes capable of hydrolyzing agars have already been isolated. This capacity to digest agar has been attributed to the genera Pseudomonas (MORRICE et al., Eur. J. Biochem. 137, 149-154, (1983)), Streptomyces (HODGSON and CHATER, J. Gen. Microbiol. 124, 339-348, (1981)), Cytophaga (VAN DER MEULEN and HARDER, J. Microbiol. 41, 431-447, (1975)) and Vibrio (SUGANO et al., Appl. Environ. Microbiol. 59, 1549-1554, (1993)). Several β-agarase genes have already been isolated. Thus BELAS et al. isolated the gene of an agarase from Pseudomonas atlantica (Appl. Environ. Microbiol. 54, 30-37, (1988)). BUTTNER et al. isolated an agarase from Streptomyces coelicolor and sequenced the corresponding gene (Mol. Gen. Genet. 209, 101-109, (1987)). SUGANO et al. cloned and sequenced two different agarase genes from Vibrio sp. JT0107, which they called agaA (Appl. Environ. Microbiol. 59, 3750-3756, (1993)) and agaB (Biochimica et Biophysica Acta 1 218, 105-108, (1994)).

The Applicant has now isolated, from the red alga Delesseria sanguinea, a bacterial strain which has agarase activity.

This strain was deposited in the DSMZ Collection (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures)) on May 8, 1998 under the number DSM 12170. It forms the first subject of the present invention.

Taxonomic investigation of this strain, performed by techniques well known to those skilled in the art, shows that it belongs to the genus Cytophaga (bacteria of the CFB or “Cytophaga/Flexibacter/Bacteroides” group). In fact, this strain develops by spreading and has yellow colonies encrusted in the agar, which is then liquefied. The bacterium is a Gram-negative bacterium and has the shape of a non-mobile rod of 0.3-0.4×3.0-8.0 μm×μm. When a drop of culture of the strain is inoculated at the center of an agar dish, the colony develops with concentric growth of the margin and this mobility is not inhibited by diethyl ether, which is an inhibitor of the flagellar apparatus. The strain is aerobic and has an oxidative metabolism. It produces flexirubin, which is a pigment rarely found in isolates of marine Cytophaga but present in non-marine Cytophaga. It is capable of assimilating various carbon sources and degrading several types of macromolecule such as agar, carrageenan, starch and gelatin.

The Applicant carried out an in-depth study to find out what species this strain belonged to. Thus it determined the percentage guanine and cytosine composition of the DNA of the strain of the invention and found that the values were between 43 and 49%. It also sequenced its 16S DNA by the method well known to those skilled in the art for finding out the taxonomic position of a strain (FOX et al., Int. J. Syst. Bacteriol. 22, 44-57, (1977)). The sequencing result shows that the strain of the invention is very similar to Cytophaga uliginosa. (There is a 99% similarity of sequence between the 16S DNA of C. uliginosa and that of the strain of the invention.) However, DNA/DNA hybridization between the two strains (45%) shows that they are different species.

Furthermore, the strain of the invention has similar morphological, biochemical and physiological characteristics to the strain Pseudomonas drobachiensis nov. comb. isolated by HUMM (Duke Univ. Mar. Stn. Bull. 3, 43-75, (1946)). It was therefore named Cytophaga drobachiensis.

The Applicant also isolated two genes with β-agarase activity from Cytophaga drobachiensis DSM 12170.

Thus the present invention further relates to the novel agaA gene coding for a β-agarase, which has the DNA sequence SEQ ID No. 1.

It further relates to the novel agaB gene coding for a β-agarase, which has the DNA sequence SEQ ID No. 3.

These two genes code for two different β-agarases produced by C. drobachiensis DSM 12170, namely the β-agarases called proteins AgaA and AgaB.

The present invention further relates to the nucleic acid sequences, namely the genomic DNA sequences and the DNA or mRNA sequences, which comprise or consist of a concatenation of nucleotides coding for the protein AgaA or the protein AgaB or for any one of their peptide fragments as defined below.

The invention therefore relates to:

All the nucleic acid sequences coding for the protein AgaA in its entirety or for one or more of its peptide fragments. These sequences are preferably represented by:

a) the DNA sequence SEQ ID No. 1 coding for the protein AgaA, and its fragments coding for the peptide fragments of said protein;

b) the DNA sequences which hybridize under specific stringency conditions with the above sequence or one of its fragments;

c) the DNA sequences which, because of the degeneracy of the genetic code, are derived from one of the sequences a) and b) above and code for the protein AgaA or the fragments of said protein; and

d) the corresponding mRNA sequences.

All the nucleic acid sequences coding for the protein AgaB in its entirety or for one or more of its peptide fragments. These sequences are preferably represented by:

a) the DNA sequence SEQ ID No. 3 coding for the protein AgaB, and its fragments coding for the peptide fragments of said protein;

b) the DNA sequences which hybridize under specific stringency conditions with the above sequence or one of its fragments;

c) the DNA sequences which, because of the degeneracy of the genetic code, are derived from one of the sequences a) and b) above and code for the protein AgaB or the fragments of said protein; and

d) the corresponding mRNA sequences.

The present invention further relates to the nucleic acid sequence SEQ ID No. 5 coding for the specific peptide fragment AgaA′, which will be described below. This sequence corresponds to nucleic acids 223-1050 of SEQ ID No. 1.

The invention therefore further relates to the nucleic acid sequences coding for said peptide fragment AgaA′ and its peptide fragments, which are represented by:

a) the DNA sequence SEQ ID No. 5 coding for the peptide fragment AgaA′, and its fragments coding for the peptide fragments of said peptide fragment AgaA′;

b) the DNA sequences which hybridize under specific stringency conditions with the above sequence or one of its fragments;

c) the DNA sequences which, because of the degeneracy of the genetic code, are derived from one of the sequences a) and b) above and code for the peptide fragment AgaA′ or the fragments of said fragment; and

d) the corresponding mRNA sequences.

The nucleic acids according to the invention can be prepared by chemical synthesis or genetic engineering using the techniques well known to those skilled in the art and described for example in SAMBROOK et al. (“Molecular Cloning: a Laboratory Manual”, published by Cold Spring Harbor Press, N.Y., 1989).

For example, the DNA sequences according to the invention can be synthesized by amplifying the genes of Cytophaga drobachiensis by the PCR (polymerase chain reaction) method, as described for example by GOBLET et al. (Nucleic Acid Research 17, 2144, (1989)), using, as primers, synthetic oligonucleotides defined from the DNA sequence SEQ ID No. 1 or SEQ ID No. 3.

The nucleic acid fragment amplified in this way can then be cloned into an expression vector by the techniques described in MANIATIS et al. (Molecular Cloning. A laboratory manual, New York (1982)).

The invention further relates to the prokaryotic cells and eukaryotic cells transformed with the aid of an expression vector containing a nucleic acid sequence according to the invention. This expression vector, which can be e.g. in the form of a plasmid, must contain, in addition to the nucleic acid sequence of the invention, the means necessary for its expression, such as, in particular, a promoter, a transcription terminator, an origin of replication and, preferably, a selection marker. The transformation of prokaryotic cells and eukaryotic cells is a technique well known to those skilled in the art, who will easily be able to determine, as a function of the microorganism to be transformed, the means necessary for expression of the DNA sequence according to the invention.

The preferred prokaryotic microorganisms for the purposes of the invention are Escherichia coli and Bacillus subtilis.

The cells of Aspergillus niger, Trichoderma viridae or Pichia pastoris may be mentioned in particular as examples of eukaryotic cells which are suitable for the purposes of the invention.

The present invention further relates to the novel protein AgaA of C. drobachiensis, which comprises SEQ ID No. 2.

It further relates to the novel protein AgaB of C. drobachiensis, which comprises SEQ ID No. 4.

The novel protein AgaA is composed of 539 amino acids and has a theoretical molecular weight of 60.001 kDa. After removal of the signal peptide, this protein has a calculated molecular weight of 57.768 kDa.

The novel protein AgaB is composed of 353 amino acids. After removal of the signal peptide, this protein has a calculated molecular weight of 40.680 kDa.

The present invention further relates to the peptide fragments of the proteins AgaA and AgaB which result from the addition, suppression and/or replacement of one or more amino acids, said peptide fragments having conserved the β-agarase activity.

The present invention further relates to the peptide fragment AgaA′, which has SEQ ID No. 6.

This peptide fragment AgaA′, composed of 276 amino acids, corresponds to amino acids 20-295 of the protein AgaA.

The invention further relates to the peptide fragments of AgaA′ which result from the addition, suppression and/or replacement of one or more amino acids, said peptide fragments having conserved the β-agarase activity.

The proteins and peptide fragments according to the invention can be obtained by the techniques of genetic engineering comprising the following steps:

culture of prokaryotic cells or eukaryotic cells transformed by an expression vector possessing a nucleic acid sequence according to the invention; and

recovery of the protein or peptide fragment produced by said cells.

These techniques are well known to those skilled in the art and further details may be obtained by reference to the following work: Recombinant DNA Technology I, editors: Ales Prokop, Raskesh K. Bajpai; Annals of the New York Academy of Sciences, volume 646, 1991.

The peptide fragments can also be prepared by conventional chemical peptide synthesis well known to those skilled in the art.

The invention will now be described in detail with the aid of the experimental section below.

The techniques described in these Examples, which are well known to those skilled in the art, are largely explained in detail in the work by SAMBROOK et al. (supra) or in the work by MANIATIS et al. (supra).

The following description will be understood more clearly with the help of FIGS. 1 to 6, in which:

FIG. 1 is a photograph of an SDS-PAGE electrophoresis gel of the culture supernatant of C. drobachiensis of the invention;

FIGS. 2A and 2B show the physical maps of the genomic clones of Cytophaga drobachiensis which have agarase activity;

FIGS. 3A and 3B give the nucleotide and amino acid sequences deduced from the genes of agarase A (SEQ ID NO: 1) (FIG. 3A) and agarase B (SEQ ID NO: 3) (FIG. 3B) originating from C. drobachiensis;

FIG. 4 shows the alignment of the protein AgaA (top line) (SEQ ID NO: 2) and the protein AgaB (bottom line) (SEQ ID NO: 4) originating from the C. drobachiensis strain according to the invention;

FIG. 5 shows the hydrophobic cluster analysis (HCA) of the agarase genes and other genes of glycoside hydrolases; and

FIGS. 6A to 6C show the elution profiles of the products resulting from the hydrolysis of neoagarododecaose by the agarases originating from the C. drobachiensis strain according to the invention.

EXAMPLE 1

Isolation, Culture of the Strain Cytophaga drobachiensis DSM 12170 and Extraction of its DNA

The strain DSM 12170 was isolated from living fronds of the red alga Delesseria sanguinea, the isolation being effected on a Petri dish on Zobell's medium (ZOBELL, J. Mar. Res. 4, 41-75, (1941)) containing 2% of i-carrageenan.

The strain was cultured at 25° C. on Zobell's medium (ZOBELL, J. Mar. Res. 4, 41-75, (1941)).

The protocol employed to extract the DNA from the strain Cytophaga drobachiensis DSM 12170 is derived from that of Marmur (MARMUR, J. Mol. Biol. 3, 208-218, (1961)) and is described in detail below.

After culture, the bacteria were centrifuged at 3000 g for 15 min and then washed in sterile seawater. The cells were subjected to a final centrifugation, identical to the previous one, and were treated immediately or frozen at −20° C.

5 to 10 g of cells, depending on the cell concentration (moist weight after centrifugation), were taken up in 25 ml of Sph buffer (50 mM Tris-HCl, pH 8; 25% sucrose) and then in 5 ml of TES buffer (50 mM Tris-HCl, pH 8; 5 mM ethylenediaminetetraacetic acid; 50 mM sodium chloride) and 50 mg of lysozyme were added. Spheroplasts appeared after incubation for 15 min at room temperature.

The DNA was immediately protected by adding 100 mM ethylenediaminetetraacetic acid (final concentration), and incubation was continued in ice for a further 10 min.

Lysis was brought to completion by adding 2% of sodium dodecylsulfate (final concentration) and 25 ml of lysis solution (50 mM Tris-HCl, pH 8; 100 mM ethylenediaminetetraacetic acid; 100 mM sodium chloride).

The proteins were fully denatured by incubation for 1 hour at 50° C. in the presence of 40 mg of proteinase K. When this incubation was complete, 1 M sodium perchlorate (final concentration) was added to break the DNA/protein bonds.

The solution was deproteinized by being shaken in the presence of 0.5 volume of saturated phenol for 5 min. The shaking was carried out by hand and had to be sufficiently vigorous to form an emulsion (without which no extraction could take place) but not so vigorous as to tear the DNA. The deproteinization was continued for a further 5 min after adding 0.5 volume of chloroform/isoamyl alcohol (24/1). The proteins were concentrated at the interface between the aqueous phase and the organic phase by centrifugation at 10,000 g for 15 min at room temperature.

The aqueous phase containing the nucleic acids was transferred to a clean tube using a pipette whose tip had been enlarged so as not to tear the DNA. The deproteinization was continued and the traces of phenol were extracted from the aqueous phase by shaking the solution for 5 min in the presence of 1 volume of chloroform/isoamyl alcohol (24/1).

After centrifugation at 10,000 g for 5 min at room temperature, the aqueous phase was withdrawn with the same precautions as above, and the nucleic acids were precipitated by gently pouring in 0.6 volume of isopropanol (to form two phases). The high-molecular DNA was recovered with a glass rod, washed in 70% ethanol, dehydrated in absolute ethanol and dried in air.

After drying, the DNA was dissolved in 20 ml of TE buffer (10 mM Tris-HCl, pH 8; 1 mM ethylenediaminetetraacetic acid). This took about 12 hours and could be facilitated by heating to 50° C. When the solution obtained was opalescent—a sign of substantial contamination with proteins—the latter were efficiently removed by passing a fraction of the DNA over a cesium chloride gradient in the presence of ethidium bromide. After this passage over the gradient and removal of the ethidium bromide, the resulting DNA was quantified. It could be stored at 4° C. or frozen at −20° C.

The DNA composition, expressed as the molar percentage of guanine+cytosine (mol % of G+C), was determined by ULITZUR's spectroscopic method (Biochem. Biophys. Acta 272, 1-11, (1972)) and the cesium chloride gradient method in the presence of 2′-[4-hydroxyphenyl]-5-[4-methylpiperazin-1-yl]-2,5′-bi-1H-benzimidazole (Hoechst 33258/Sigma) (KARLOVSKY and DE COCK, Anal. Biochem. 194, 192-197, (1991)). In the first case it is 44±1% (mean of 2 manipulations) and in the second case it is 48.8%. This molar percentage of G+C was calculated using the DNA of E. coli as the standard reference.

EXAMPLE 2

Sequencing of the 16S DNA of Cytophaga drobachiensis

The 16S DNA was amplified by PCR using the genomic DNA of the C. drobachiensis strain as the template and Taq polymerase (Promega) as the enzyme. The typical PCR reaction mixture, with a volume of 50 μl, had the following composition: 100 ng of template, 10 ng of each of the two oligonucleotides specific for the 16S DNA of the Bacteria kingdom, 200 mM of each of the dNTPs (dNTP being deoxyribonucleoside triphosphate), 1.5 mM MgCl₂, Taq buffer and 2.5 U of enzyme. The different PCR steps were as follows:

6 min at 95° C. (once),

1.5 min at 95° C.; 1.5 min at 54° C.; 2.5 min at 72° C. (25 times),

8.5 min at 72° C. (polymerization step).

The product obtained by PCR was either cloned first and then sequenced, or sequenced directly by PCR using Thermosequenase (Amersham) as the enzyme, with different oligonucleotides specific for the 16S DNA, labeled at the 5′ end with Texas red. The different PCR steps were as follows:

5 min at 97° C. (once),

1 min at 97° C.; 1 min at 54° C.; 1 min at 61° C. (25 times).

This sequencing, which reveals the taxonomic position of the strain, showed that the strain according to the invention was phylogenetically very close to Cytophaga uliginosa.

EXAMPLE 3

Demonstration and Purification of the Agarase Activities in the Strain Cytophaga drobachiensis DSM 12170

The agarase activity of the strain was induced in a Zobell medium supplemented with 2.5 mg/l of agar. A strain is considered to exhibit agarase activity when it digests the agar on which it develops.

The strains with agarase activity were cultured in the above medium at 20° C. The culture was centrifuged at 1000 g for 20 min. The culture supernatant was recovered and concentrated to 50 ml by tangential ultrafiltration (cut-off threshold: 10 kDa), this operation being followed by precipitation with ammonium sulfate. The protein residue was resuspended in 9 ml of MES buffer (MES being 2-[N-morpholino]ethanesulfonic acid). 2 ml of Sepharose CL6B were then added for carrying out affinity chromatography. Two fractions were recovered, one of which bound to the Sepharose column.

The agarase activity was tested by assaying the reducing sugars according to the technique of KIDBY D. K. & DAVIDSON D. J. (Annal. Biochem. vol. 55, 321-325, (1973)) in the supernatant before affinity chromatography (which is quite obviously positive) and in the two fractions obtained after chromatography. Agarase activity was detected in each fraction.

SDS-PAGE electrophoresis was carried out on the fraction bound to the column. This gave a main band with a mean molecular weight of 31 kDa (FIG. 1). This protein was microsequenced. The sequence of the internal peptide obtained was found in the amino acid sequence deduced from the agaA gene (FIG. 3A).

EXAMPLE 4

Cloning of the Agarase Genes

A genomic DNA library of the C. drobachiensis strain was constructed. 4 to 10 kb fragments originating from partial digestion of the chromosomal DNA by NdeII were fractionated on a sucrose gradient. These fragments were inserted into the BamHI site of plasmid pAT153 (TWIGG and SHERRATT, Nature 283, 216, (1980)).

The recombinant clones (about 6000) of the strain E. coli DH5α (SAMBROOK et al., supra) were independently inoculated onto microtiter plates in LBA medium (Luria-Bertani medium (MANIATIS et al., supra) supplemented with ampicillin at a concentration of 50 μg/ml). After incubation overnight at 37° C., these clones were plated at 22° C. on Zd medium (5 mg/l of bactotryptone, 1 mg/l of yeast extract, 10 mg/l of NaCl, pH 7.2) supplemented with 50 μg/ml of ampicillin in order to observe the agarase production (hole in the gelose when there is agarase production).

In two months of culture at 22° C., 4 independent colonies, called pAC1 to pAC4, made a hole in the substrate.

The maps of the plasmids corresponding to these colonies are shown in FIGS. 2A and 2B, in which:

the thin lines represent the pAT153 regions, the emboldened segments represent the C. drobachiensis inserts and the white rectangles represent the agarase genes; and

the various abbreviations have the following meanings:

B/S: BamHI-Sau3A cloning site

B: BamHI

Bg: BglII

C: ClaI

E: EcoRI

H: HindIII

K: KnpI

Nc: NcoI

Nd: NdeI

Ps: PstI

Pv: PvuII

Sa: SalI

Sp: SphI

X: XbaI

The mapping of these plasmids therefore shows the presence of two different common fragments, suggesting the presence of at least two agarase genes in the genome of C. drobachiensis. Plasmids pAC1 and pAC2 share a common SalI-PstI fragment of 5 kb (delimited by the broken lines in FIG. 2A) and plasmids pAC3 and pAC4 share a common ClaI-PstI fragment of 5 kb (delimited by the broken lines in FIG. 2B).

The two fragments were subcloned into phagemid pBluescript (Stratagène) and are called pASP5 and pACP5, as indicated in FIGS. 2A and 2B. These two subclones have an agarase+phenotype.

EXAMPLE 5

Analysis of the Nucleotide Sequence of the Agarase Genes

Plasmids pASP5 and pACP5 were used to determine, on both strands, the nucleotide sequences of the agarase structural genes.

This sequencing was effected by a technique well known to those skilled in the art, namely Sanger's method (SANGER et al., Proc. Natl. Acad. Sci. 74, 5463-5467, (1977)), which is also called the dideoxynucleotide method.

The pASP5 insert was sequenced over 2980 bp from the BamHI site to the HindIII site (delimited by the letters B/S and H in FIG. 2A). It contains a single open reading frame (ORF) of 1617 bp, called the agaA gene. This gene has SEQ ID No. 1.

The nucleic acid sequence obtained is illustrated in FIG. 3A. Two hexamers, TaGAaA and TATAtT, compatible with the “−35” and “−10” consensus promoters of E. coli—the capital letters corresponding to the consensus promoter of E. coli (ROSENBERG, M. & COURT, D., Ann. Rev. 13, 319-353, (1979))—and separated by 15 nucleotides, are found 62 nucleotides upstream from the putative start codon of the agaA gene. In the untranslated 3′ region, a transcription termination loop is found downstream from the TAA stop codon, followed by three thymidine residues.

The pACP5 insert was sequenced over 2440 bp between the two EcoRI sites (delimited by the two letters E in FIG. 2B). It contains a single complete ORF of 1059 bp, called the agaB gene, and a partial ORF. This agaB gene has SEQ ID No. 3.

The nucleic acid sequence obtained is illustrated in FIG. 3B. Two hexamers, TTGAgA and TATtcT, compatible with the “−35” and “−10” consensus promoters of E. coli and separated by 17 nucleotides, are found 43 nucleotides upstream from the putative start codon of the agaB gene. In the untranslated 3′ region, a transcription termination loop is found downstream from the TAA stop codon, followed by four thymidine residues. The second, partial ORF is found downstream from the agaB gene. Two hexamers, TTGACc and TtaAtT, separated by 17 nucleotides, are also found 39 nucleotides upstream from the putative start codon of the second ORF.

The Chargaff coefficient (GC%) of each of the agarase A and B genes is between 41 and 45%, which is in agreement with that of the genus Cytophaga found by REICHENBACH et al. (30-45%; Genus Cytophaga, in Bergey's Manual of systematic bacteriology, 2015-2050, (1989)).

EXAMPLE 6

Analysis of the Amino Acid Sequence Deduced from the Agarase Genes

The translation product of the agaA gene is a protein of 539 amino acids with a theoretical molecular weight of 60.001 kDa. The deduced amino acid sequence, SEQ ID No. 2, comprises the internal peptide determined from the microsequencing of the purified agarase A (underlined in FIG. 3A). As indicated by analysis of the hydropathy profile (KYTE and DOOLITLE, J. Mol. Biol. 157, 105-132, (1982)), the N-terminal part of the protein corresponds to a very hydrophobic domain, suggesting that this domain is the signal peptide (VON HEIJNE, Eur. J. Biochem. 133, 17-21, (1983); J. Mol. Biol. 184, 99-105, (1985)). According to Von Heijne's “(−3,−1)” rule, the most probable cleavage site of the signal peptidase is assigned between Ala19 and Ala20.

It should be noted that the molecular weight of the protein AgaA calculated after removal of the signal peptide, i.e. about 57.768 kDa, is greater than the molecular weight initially determined by SDS-PAGE electrophoresis, i.e. 31 kDa (cf. FIG. 1). This difference indicates a possible transformation after translation, which would remove a large part of the C-terminal end of the protein.

The translation product of the agaB gene is a protein of 353 amino acids with a calculated molecular weight of 40.680 kDa and with the deduced amino acid sequence SEQ ID No. 4. Analysis of the hydropathy profile shows a very hydrophobic N-terminal segment in a domain of about 20 amino acids. However, no cleavage site exists according to Von Heijne's “(−3,−1)” rule (supra). This segment therefore seems to be non-cleavable. The signal peptide search results obtained from the software PSORT (Nakai's expert system PSORT) (NAKAI & KANEHISA, Proteins, Structure, Function and Genetics 11, 95-110, (1991)) suggest that the protein possesses a non-cleavable N-terminal signal sequence acting as a transmembrane anchor. It should also be noted that the sequence LVFCCALLLGCGD is in perfect agreement with the signature of the N-terminal end of prokaryotic lipoproteins (Prosite PS00013; BAIROCH et al., Nucl. Acids Res. 24, 189-196, (1995)). In this case a cleavage site would be possible between the residues G17 and C18. These results suggest that AgaB could be a lipoprotein located in the internal membrane of the cell.

The ORF which follows the agaB gene codes for a protein which has a significant homology with the DnaJ protein family (OHKI et al., J. Biol. Chem. 261, 1778-1781, (1986)) (FIG. 3B).

EXAMPLE 7

Similarities of Sequence Between the Proteins AgaA and AgaB of C. drobachiensis and with Other β-glycanases

The similarities of sequence between the proteins AgaA and AgaB are illustrated in FIG. 4. The protein AgaA has a 44.5% identity and a 65.7% similarity with the protein AgaB. Numerous domains are fairly similar in the primary sequences from Ile110 to Val287 (numbering of the agarase A sequence). In particular, in one of the best conserved units, two glutamic acid residues are present and are separated by 4 amino acids (Glu147 and Glu152 in the AgaA sequence and Glu184 and Glu189 in the AgaB sequence, emboldened in FIG. 4). This organization is characteristic of the catalytic site of family 16 of glycoside hydrolases (HENRISSAT, Biochem. J. 280, 309-316, (1991)).

No similarity of sequence was found with the agarases of the strain Vibrio sp. JT0107 (SUGANO et al., Appl. Environ. Microbiol. 59, 3750-3756, (1993); Biochim. Biophys. Acta 1218, 105-108, (1994)).

Nevertheless, the agarases (AgaA and AgaB) share significant sequence identities with the β-agarases of Alteromonas atlantica GenBank M73783 (BELAS et al., J. Bacteriol. 54, 30-37, (1988)) (53.5% and 48% with AgaA and AgaB respectively) and those of Streptomyces coelicolor (BUTTNER et al., Mol. Gen. Genet. 209, 101-109, (1987)) (33% with AgaA and AgaB).

These similarities are also demonstrated by means of the HCA (hydrophobic cluster analysis) method (LEMESLE-VARLOOT et al., Biochimie 72, 555-574, (1990)). FIG. 5 illustrates the HCA comparison between the agarases AgaA and AgaB, namely Agar A Cd and Agar B Cd, respectively, in the Figure, and other enzymes of family 16 of glycoside hydrolases, namely the β-agarase of Alteromonas atlantica (Agar Aa), the β-agarase of Streptomyces coecicolor (Agar Sc), the κ-carrageenase of C. drobachiensis (Kap Cd), the laminarinase of Rhodothernus marinus (Lam Rm), the lichenase of Bacillus macerans (Lich Bm) and the xyloglucan endotransglycosylase of Arabidopsis thaliana (XET At).

The two catalytic residues Glu present in the lichenase of Bacillus macerans were taken as anchoring points for the HCA comparison, and the sequences were segmented taking the known three-dimensional structure of this lichenase as the reference.

Thirteen segments of different structure (I-XIII) are shown in FIG. 5, segments I, II, IX, X, XI and XIII appearing to be the best conserved. It may be noted that segment VI is specific for the agarases in this family of glycoside hydrolases and that the catalytic site is located in the segment of structure III.

EXAMPLE 8

Substrate Specificities of the Recombinant Agarases AgaA and AgaB

The substrate specificities of the agarases of the invention were studied by analyzing the products resulting from the degradation of neoagarododecaose by the recombinant agarases AgaA and AgaB.

The neoagarododecaose was prepared as follows: Agarose was hydrolyzed with agarase using 0.32 U/mg of polymer. The resistant fraction was precipitated in isopropanol and the soluble oligosaccharides were fractionated by preparative exclusion chromatography on Bio-gel P2 (95 cm×4.4 cm; 25° C.; eluent: distilled water). Detection was effected with an apparatus for recording the differential refractive index (ROCHAS & HEYRAUD, Polymer Bull. 5, 81-86, (1981)). The oligomeric fraction corresponding to the neoagarododecaose was concentrated on a rotary evaporator and lyophilized.

The recombinant clones of E. coli containing plasmids pAC1 and pAC4 (with agarase A and agarase B activity, respectively) were cultured for 12 hours at 37° C. in 1 liter of LB medium (Luria-Bertani medium). The cells were centrifuged at 2000 g for 20 minutes, suspended in 30 ml of MES buffer and burst with the aid of a French press at 20,000 psi. After centrifugation at 20,000 g for 1 hour, the cell fragments were discarded and the volume of the supernatant was reduced to 5 ml using an ultrafiltration cell (Amicon, 10 kDa cut-off threshold).

500 μl of each extract obtained in this way were added to 1 ml of neoagarododecaose in MES buffer (50 mg/ml) and the mixtures were incubated at 37° C. for 18 hours. The degree of polymerization of the final products was determined by HPAE chromatography using a pulsed electrochemical detector and an anion exchange column (Carbo-PAC PA100, Dionex) under the following conditions: flow rate: 1 ml/min; buffer A: 150 mM NaOH; buffer B: 500 mM sodium acetate in 150 mM NaOH; gradient:

0 to 5 min: 70% of A, 30% of B;

5 to 16 min: 40% of A, 60% of B;

16 to 20 min: 100% of B.

The results obtained by HPAE chromatography (high performance anion exchange chromatography) are illustrated in FIGS. 6A to 6C, in which the various abbreviations have the following meanings:

nC: nanocoulomb

DP1: neoagarobiose

DP2: neoagarotetraose

DP3: neoagarohexaose

DP4: neoagarooctaose

DP5: neoagarodecaose

DP6: neoagarododecaose

DP7: neoagarotetradecaose

DP8: neoagarohexadecaose

The final products resulting from the hydrolysis of neoagarododecaose by agarase A and agarase B are shown in FIGS. 6B and 6C respectively. In comparison with neoagarododecaose without enzyme (FIG. 6A), the elution profile after 18 hours of digestion shows neoagarotetraose (DP2) to be the major product and neoagarohexaose (DP3) to be the minor product in both cases (AgaA and AgaB).

6 1 2035 DNA Cytophaga drobachiensis CDS (166)..(1782) 1 ttattcttac taatattgta ggaaaattta acacaaaaaa catctttgtt cagtttttgt 60 cgagttggta aaacctagaa aacagacacg gcattgtata tttggcgatg attcatctgt 120 ttgtttgttg aatacatttt tattaacccc taaaattaca ttatc atg aaa aaa aat 177 Met Lys Lys Asn 1 tat ctt tta ctg tat ttt att ttt ctt ttg tgt ggc tct atc gct gca 225 Tyr Leu Leu Leu Tyr Phe Ile Phe Leu Leu Cys Gly Ser Ile Ala Ala 5 10 15 20 cag gac tgg aac gga att cct gta cct gcc aat ccc gga aat ggt atg 273 Gln Asp Trp Asn Gly Ile Pro Val Pro Ala Asn Pro Gly Asn Gly Met 25 30 35 act tgg caa tta cag gat aat gtt tcg gat agt ttt aat tac aca agt 321 Thr Trp Gln Leu Gln Asp Asn Val Ser Asp Ser Phe Asn Tyr Thr Ser 40 45 50 agt gaa gga aat agg cct act gcc ttt act agt aaa tgg aaa cct tcc 369 Ser Glu Gly Asn Arg Pro Thr Ala Phe Thr Ser Lys Trp Lys Pro Ser 55 60 65 tat atc aat gga tgg act ggt cct gga tca aca att ttt aat gcc gcg 417 Tyr Ile Asn Gly Trp Thr Gly Pro Gly Ser Thr Ile Phe Asn Ala Ala 70 75 80 cag gca tgg acc aat ggt tct caa ttg gca att cag gca caa cca gca 465 Gln Ala Trp Thr Asn Gly Ser Gln Leu Ala Ile Gln Ala Gln Pro Ala 85 90 95 100 ggg aat gga aaa tct tac aac gga att atc acc tcc aaa aat aag atc 513 Gly Asn Gly Lys Ser Tyr Asn Gly Ile Ile Thr Ser Lys Asn Lys Ile 105 110 115 cag tac ccg gtg tat atg gaa att aag gcc aag ata atg gac cag gta 561 Gln Tyr Pro Val Tyr Met Glu Ile Lys Ala Lys Ile Met Asp Gln Val 120 125 130 cta gca aat gct ttc tgg acc ttg act gac gac gag act cag gaa att 609 Leu Ala Asn Ala Phe Trp Thr Leu Thr Asp Asp Glu Thr Gln Glu Ile 135 140 145 gat att atg gaa ggc tat ggc agt gat cgg ggg gga act tgg ttc gcc 657 Asp Ile Met Glu Gly Tyr Gly Ser Asp Arg Gly Gly Thr Trp Phe Ala 150 155 160 caa aga atg cat ttg agc cac cat aca ttt att cgt aac ccc ttt acg 705 Gln Arg Met His Leu Ser His His Thr Phe Ile Arg Asn Pro Phe Thr 165 170 175 180 gat tat cag cct atg gga gac gct aca tgg tat tac aac gga ggt aca 753 Asp Tyr Gln Pro Met Gly Asp Ala Thr Trp Tyr Tyr Asn Gly Gly Thr 185 190 195 cca tgg cgt tca gca tat cac cgt tat gga tgt tat tgg aaa gat cca 801 Pro Trp Arg Ser Ala Tyr His Arg Tyr Gly Cys Tyr Trp Lys Asp Pro 200 205 210 ttt aca ttg gaa tat tat att gac ggg gta aag gtt aga acg gtc aca 849 Phe Thr Leu Glu Tyr Tyr Ile Asp Gly Val Lys Val Arg Thr Val Thr 215 220 225 aga gcc gaa att gat cct aat aat cat ctc ggc gga aca ggg ttg aat 897 Arg Ala Glu Ile Asp Pro Asn Asn His Leu Gly Gly Thr Gly Leu Asn 230 235 240 cag gca aca aat att att att gat tgt gaa aat caa aca gat tgg agg 945 Gln Ala Thr Asn Ile Ile Ile Asp Cys Glu Asn Gln Thr Asp Trp Arg 245 250 255 260 ccc gcg gct act caa gaa gaa ctg gcc gat gat agc aaa aat atc ttc 993 Pro Ala Ala Thr Gln Glu Glu Leu Ala Asp Asp Ser Lys Asn Ile Phe 265 270 275 tgg gtc gat tgg ata cgt gtg tac aag cct gtt gcg gta agt gga ggt 1041 Trp Val Asp Trp Ile Arg Val Tyr Lys Pro Val Ala Val Ser Gly Gly 280 285 290 gga aac aac ggt aac gac ggt gcc act gaa ttt caa tat gat tta gga 1089 Gly Asn Asn Gly Asn Asp Gly Ala Thr Glu Phe Gln Tyr Asp Leu Gly 295 300 305 acg gac acc tcg gca gta tgg cca ggg tat aca cgg gtt tcc aac acc 1137 Thr Asp Thr Ser Ala Val Trp Pro Gly Tyr Thr Arg Val Ser Asn Thr 310 315 320 act agg gct ggt aat ttt gga tgg gcg aac acc aat gac atc gga tca 1185 Thr Arg Ala Gly Asn Phe Gly Trp Ala Asn Thr Asn Asp Ile Gly Ser 325 330 335 340 aga gat cgt ggg gct tct aac gga agg aac aat ata aac cgt gat att 1233 Arg Asp Arg Gly Ala Ser Asn Gly Arg Asn Asn Ile Asn Arg Asp Ile 345 350 355 aat ttt agt tca caa act agg ttc ttc act caa gac cta tcc aat ggc 1281 Asn Phe Ser Ser Gln Thr Arg Phe Phe Thr Gln Asp Leu Ser Asn Gly 360 365 370 act tat aac gta ttg atc act ttt ggg gac acc tat gcc cga aaa aat 1329 Thr Tyr Asn Val Leu Ile Thr Phe Gly Asp Thr Tyr Ala Arg Lys Asn 375 380 385 atg aac gtc gcg gcc gaa ggg caa aat aaa tta aca aac ata aac acc 1377 Met Asn Val Ala Ala Glu Gly Gln Asn Lys Leu Thr Asn Ile Asn Thr 390 395 400 aat gcc ggg caa tat gtt agt agg tcg ttt gac gta aat gtc aac gac 1425 Asn Ala Gly Gln Tyr Val Ser Arg Ser Phe Asp Val Asn Val Asn Asp 405 410 415 420 gga aaa cta gat ttg cga ttt tca gtt ggt aat ggc ggg gat gtg tgg 1473 Gly Lys Leu Asp Leu Arg Phe Ser Val Gly Asn Gly Gly Asp Val Trp 425 430 435 tcc att aca aga atc tgg att aga aaa gtt acg agc aac agc gct aat 1521 Ser Ile Thr Arg Ile Trp Ile Arg Lys Val Thr Ser Asn Ser Ala Asn 440 445 450 ttg tta gcg gca aaa gga tta aca ttg gaa gat cct gtg gaa act acg 1569 Leu Leu Ala Ala Lys Gly Leu Thr Leu Glu Asp Pro Val Glu Thr Thr 455 460 465 gaa ttt tta tat cct aac ccc gca aaa aca gat gat ttt gtg act gtt 1617 Glu Phe Leu Tyr Pro Asn Pro Ala Lys Thr Asp Asp Phe Val Thr Val 470 475 480 ccc aat agt gaa att gga agt agt ata atc atc tat aat agt gca ggt 1665 Pro Asn Ser Glu Ile Gly Ser Ser Ile Ile Ile Tyr Asn Ser Ala Gly 485 490 495 500 caa gta gtg aaa aaa gta agt gtg gtt tcc gaa aat cag aaa ata tca 1713 Gln Val Val Lys Lys Val Ser Val Val Ser Glu Asn Gln Lys Ile Ser 505 510 515 cta gaa gga ttt gct aaa gga atg tac ttt atc aat ttg aat ggt cag 1761 Leu Glu Gly Phe Ala Lys Gly Met Tyr Phe Ile Asn Leu Asn Gly Gln 520 525 530 agt aca aaa ctt att gtc caa taaacacaat aacaatttca attaaacgac 1812 Ser Thr Lys Leu Ile Val Gln 535 aaaggcgctc tgatgataca gaaaggcctt tgtcgttttt taagttactt caggaaccaa 1872 gataaatttt taggtggtat tgttagcttc ttctaactag aatatgatct gtgttttgcg 1932 ggcttcttgt acttgctgta accgcttcgt ttttgtgcaa tgtcggcaca tggtgtatgc 1992 cctgtttact gggtaaatta ggtacttttc tttttgaagc tta 2035 2 539 PRT Cytophaga drobachiensis 2 Met Lys Lys Asn Tyr Leu Leu Leu Tyr Phe Ile Phe Leu Leu Cys Gly 1 5 10 15 Ser Ile Ala Ala Gln Asp Trp Asn Gly Ile Pro Val Pro Ala Asn Pro 20 25 30 Gly Asn Gly Met Thr Trp Gln Leu Gln Asp Asn Val Ser Asp Ser Phe 35 40 45 Asn Tyr Thr Ser Ser Glu Gly Asn Arg Pro Thr Ala Phe Thr Ser Lys 50 55 60 Trp Lys Pro Ser Tyr Ile Asn Gly Trp Thr Gly Pro Gly Ser Thr Ile 65 70 75 80 Phe Asn Ala Ala Gln Ala Trp Thr Asn Gly Ser Gln Leu Ala Ile Gln 85 90 95 Ala Gln Pro Ala Gly Asn Gly Lys Ser Tyr Asn Gly Ile Ile Thr Ser 100 105 110 Lys Asn Lys Ile Gln Tyr Pro Val Tyr Met Glu Ile Lys Ala Lys Ile 115 120 125 Met Asp Gln Val Leu Ala Asn Ala Phe Trp Thr Leu Thr Asp Asp Glu 130 135 140 Thr Gln Glu Ile Asp Ile Met Glu Gly Tyr Gly Ser Asp Arg Gly Gly 145 150 155 160 Thr Trp Phe Ala Gln Arg Met His Leu Ser His His Thr Phe Ile Arg 165 170 175 Asn Pro Phe Thr Asp Tyr Gln Pro Met Gly Asp Ala Thr Trp Tyr Tyr 180 185 190 Asn Gly Gly Thr Pro Trp Arg Ser Ala Tyr His Arg Tyr Gly Cys Tyr 195 200 205 Trp Lys Asp Pro Phe Thr Leu Glu Tyr Tyr Ile Asp Gly Val Lys Val 210 215 220 Arg Thr Val Thr Arg Ala Glu Ile Asp Pro Asn Asn His Leu Gly Gly 225 230 235 240 Thr Gly Leu Asn Gln Ala Thr Asn Ile Ile Ile Asp Cys Glu Asn Gln 245 250 255 Thr Asp Trp Arg Pro Ala Ala Thr Gln Glu Glu Leu Ala Asp Asp Ser 260 265 270 Lys Asn Ile Phe Trp Val Asp Trp Ile Arg Val Tyr Lys Pro Val Ala 275 280 285 Val Ser Gly Gly Gly Asn Asn Gly Asn Asp Gly Ala Thr Glu Phe Gln 290 295 300 Tyr Asp Leu Gly Thr Asp Thr Ser Ala Val Trp Pro Gly Tyr Thr Arg 305 310 315 320 Val Ser Asn Thr Thr Arg Ala Gly Asn Phe Gly Trp Ala Asn Thr Asn 325 330 335 Asp Ile Gly Ser Arg Asp Arg Gly Ala Ser Asn Gly Arg Asn Asn Ile 340 345 350 Asn Arg Asp Ile Asn Phe Ser Ser Gln Thr Arg Phe Phe Thr Gln Asp 355 360 365 Leu Ser Asn Gly Thr Tyr Asn Val Leu Ile Thr Phe Gly Asp Thr Tyr 370 375 380 Ala Arg Lys Asn Met Asn Val Ala Ala Glu Gly Gln Asn Lys Leu Thr 385 390 395 400 Asn Ile Asn Thr Asn Ala Gly Gln Tyr Val Ser Arg Ser Phe Asp Val 405 410 415 Asn Val Asn Asp Gly Lys Leu Asp Leu Arg Phe Ser Val Gly Asn Gly 420 425 430 Gly Asp Val Trp Ser Ile Thr Arg Ile Trp Ile Arg Lys Val Thr Ser 435 440 445 Asn Ser Ala Asn Leu Leu Ala Ala Lys Gly Leu Thr Leu Glu Asp Pro 450 455 460 Val Glu Thr Thr Glu Phe Leu Tyr Pro Asn Pro Ala Lys Thr Asp Asp 465 470 475 480 Phe Val Thr Val Pro Asn Ser Glu Ile Gly Ser Ser Ile Ile Ile Tyr 485 490 495 Asn Ser Ala Gly Gln Val Val Lys Lys Val Ser Val Val Ser Glu Asn 500 505 510 Gln Lys Ile Ser Leu Glu Gly Phe Ala Lys Gly Met Tyr Phe Ile Asn 515 520 525 Leu Asn Gly Gln Ser Thr Lys Leu Ile Val Gln 530 535 3 1440 DNA Cytophaga drobachiensis CDS (196)..(1254) 3 gtctttatca caattctatc ttagaattct tactaatgct gacaaaacta cggctgcaac 60 cgtgtattac gataacttct ctatcattga aaaagaagag aggccataac aattgttgag 120 tgtttgagat agagggagaa ttgaaatatt ctcccttttt atcctttttt cattttaaac 180 aaattacgta taaac atg tat tta ata tat ctt agg ttg gtc ttt tgc tgt 231 Met Tyr Leu Ile Tyr Leu Arg Leu Val Phe Cys Cys 1 5 10 gcc ctt ttg ttg ggg tgt ggc gac aat tca aaa ttt gat agt gca acg 279 Ala Leu Leu Leu Gly Cys Gly Asp Asn Ser Lys Phe Asp Ser Ala Thr 15 20 25 gat ttg ccg gtt gaa caa gaa caa gaa cag gaa acg gaa caa gag gga 327 Asp Leu Pro Val Glu Gln Glu Gln Glu Gln Glu Thr Glu Gln Glu Gly 30 35 40 gaa ccc gaa gaa agt tcg gag caa gac ctt gtc gag gag gtc gat tgg 375 Glu Pro Glu Glu Ser Ser Glu Gln Asp Leu Val Glu Glu Val Asp Trp 45 50 55 60 aag gat att ccc gta ccc gcc gat gca gga ccg aat atg aag tgg gag 423 Lys Asp Ile Pro Val Pro Ala Asp Ala Gly Pro Asn Met Lys Trp Glu 65 70 75 ttt caa gag att tcc gat aat ttt gaa tat gag gcc cct gcg gat aat 471 Phe Gln Glu Ile Ser Asp Asn Phe Glu Tyr Glu Ala Pro Ala Asp Asn 80 85 90 aag ggg agt gaa ttt ctc gaa aag tgg gac gat ttt tat cac aat gcc 519 Lys Gly Ser Glu Phe Leu Glu Lys Trp Asp Asp Phe Tyr His Asn Ala 95 100 105 tgg gca ggc cca ggg ctg acc gaa tgg aaa cgg gac agg tcc tat gta 567 Trp Ala Gly Pro Gly Leu Thr Glu Trp Lys Arg Asp Arg Ser Tyr Val 110 115 120 gcc gat ggc gag cta aag atg tgg gcg aca aga aaa ccg ggc tcc gat 615 Ala Asp Gly Glu Leu Lys Met Trp Ala Thr Arg Lys Pro Gly Ser Asp 125 130 135 140 aaa ata aac atg ggg tgc att act tct aag acc cga gtg gtc tat cct 663 Lys Ile Asn Met Gly Cys Ile Thr Ser Lys Thr Arg Val Val Tyr Pro 145 150 155 gtt tat att gaa gca agg gca aag gtc atg aac tct acc ttg gct tcg 711 Val Tyr Ile Glu Ala Arg Ala Lys Val Met Asn Ser Thr Leu Ala Ser 160 165 170 gat gtt tgg ctc tta agt gcc gat gac acc caa gag ata gat att cta 759 Asp Val Trp Leu Leu Ser Ala Asp Asp Thr Gln Glu Ile Asp Ile Leu 175 180 185 gag gca tat ggg gcc gat tat tcc gaa agt gcc gga aag gat cat tcc 807 Glu Ala Tyr Gly Ala Asp Tyr Ser Glu Ser Ala Gly Lys Asp His Ser 190 195 200 tat ttt tct aaa aag gta cac ata agc cat cac gtc ttt att cga gac 855 Tyr Phe Ser Lys Lys Val His Ile Ser His His Val Phe Ile Arg Asp 205 210 215 220 cca ttt caa gat tat caa cca aag gat gcc ggt tct tgg ttc gaa gac 903 Pro Phe Gln Asp Tyr Gln Pro Lys Asp Ala Gly Ser Trp Phe Glu Asp 225 230 235 ggc acc gtc tgg aac aaa gag ttc cat agg ttt ggt gtg tat tgg agg 951 Gly Thr Val Trp Asn Lys Glu Phe His Arg Phe Gly Val Tyr Trp Arg 240 245 250 gat cca tgg cat cta gaa tat tac ata gac ggt gtt ctg gtg agg acc 999 Asp Pro Trp His Leu Glu Tyr Tyr Ile Asp Gly Val Leu Val Arg Thr 255 260 265 gtt tcg gga aag gac att atc gac ccc aaa cac ttt acg aat aca acg 1047 Val Ser Gly Lys Asp Ile Ile Asp Pro Lys His Phe Thr Asn Thr Thr 270 275 280 gat ccc ggt aat acg gaa atc gat acc cgc acc ggt ctc aat aaa gaa 1095 Asp Pro Gly Asn Thr Glu Ile Asp Thr Arg Thr Gly Leu Asn Lys Glu 285 290 295 300 atg gat att att atc aat aca gaa gac caa act tgg cgg tct tca ccg 1143 Met Asp Ile Ile Ile Asn Thr Glu Asp Gln Thr Trp Arg Ser Ser Pro 305 310 315 gcc tcg ggt tta cag tct aat acc tat acg cca acg gac aat gaa ttg 1191 Ala Ser Gly Leu Gln Ser Asn Thr Tyr Thr Pro Thr Asp Asn Glu Leu 320 325 330 agc aat ata gaa aac aat acg ttc ggg gtc gat tgg atc agg atc tat 1239 Ser Asn Ile Glu Asn Asn Thr Phe Gly Val Asp Trp Ile Arg Ile Tyr 335 340 345 aaa cct gta gag aaa taagaaaatc cttcttttgc tttggtcgcg cccgtgagct 1294 Lys Pro Val Glu Lys 350 tatgattcgg cgctgtctaa atagttttat aaaaccatag gtagttcccc ctttgttcaa 1354 actacttgcc tatggttttt tttatgtttt attccagaaa gatgactggg gtcatatgat 1414 gttatttatc tttttcttcc cataaa 1440 4 353 PRT Cytophaga drobachiensis 4 Met Tyr Leu Ile Tyr Leu Arg Leu Val Phe Cys Cys Ala Leu Leu Leu 1 5 10 15 Gly Cys Gly Asp Asn Ser Lys Phe Asp Ser Ala Thr Asp Leu Pro Val 20 25 30 Glu Gln Glu Gln Glu Gln Glu Thr Glu Gln Glu Gly Glu Pro Glu Glu 35 40 45 Ser Ser Glu Gln Asp Leu Val Glu Glu Val Asp Trp Lys Asp Ile Pro 50 55 60 Val Pro Ala Asp Ala Gly Pro Asn Met Lys Trp Glu Phe Gln Glu Ile 65 70 75 80 Ser Asp Asn Phe Glu Tyr Glu Ala Pro Ala Asp Asn Lys Gly Ser Glu 85 90 95 Phe Leu Glu Lys Trp Asp Asp Phe Tyr His Asn Ala Trp Ala Gly Pro 100 105 110 Gly Leu Thr Glu Trp Lys Arg Asp Arg Ser Tyr Val Ala Asp Gly Glu 115 120 125 Leu Lys Met Trp Ala Thr Arg Lys Pro Gly Ser Asp Lys Ile Asn Met 130 135 140 Gly Cys Ile Thr Ser Lys Thr Arg Val Val Tyr Pro Val Tyr Ile Glu 145 150 155 160 Ala Arg Ala Lys Val Met Asn Ser Thr Leu Ala Ser Asp Val Trp Leu 165 170 175 Leu Ser Ala Asp Asp Thr Gln Glu Ile Asp Ile Leu Glu Ala Tyr Gly 180 185 190 Ala Asp Tyr Ser Glu Ser Ala Gly Lys Asp His Ser Tyr Phe Ser Lys 195 200 205 Lys Val His Ile Ser His His Val Phe Ile Arg Asp Pro Phe Gln Asp 210 215 220 Tyr Gln Pro Lys Asp Ala Gly Ser Trp Phe Glu Asp Gly Thr Val Trp 225 230 235 240 Asn Lys Glu Phe His Arg Phe Gly Val Tyr Trp Arg Asp Pro Trp His 245 250 255 Leu Glu Tyr Tyr Ile Asp Gly Val Leu Val Arg Thr Val Ser Gly Lys 260 265 270 Asp Ile Ile Asp Pro Lys His Phe Thr Asn Thr Thr Asp Pro Gly Asn 275 280 285 Thr Glu Ile Asp Thr Arg Thr Gly Leu Asn Lys Glu Met Asp Ile Ile 290 295 300 Ile Asn Thr Glu Asp Gln Thr Trp Arg Ser Ser Pro Ala Ser Gly Leu 305 310 315 320 Gln Ser Asn Thr Tyr Thr Pro Thr Asp Asn Glu Leu Ser Asn Ile Glu 325 330 335 Asn Asn Thr Phe Gly Val Asp Trp Ile Arg Ile Tyr Lys Pro Val Glu 340 345 350 Lys 5 828 DNA Cytophaga drobachiensis 5 gcacaggact ggaacggaat tcctgtacct gccaatcccg gaaatggtat gacttggcaa 60 ttacaggata atgtttcgga tagttttaat tacacaagta gtgaaggaaa taggcctact 120 gcctttacta gtaaatggaa accttcctat atcaatggat ggactggtcc tggatcaaca 180 atttttaatg ccgcgcaggc atggaccaat ggttctcaat tggcaattca ggcacaacca 240 gcagggaatg gaaaatctta caacggaatt atcacctcca aaaataagat ccagtacccg 300 gtgtatatgg aaattaaggc caagataatg gaccaggtac tagcaaatgc tttctggacc 360 ttgactgacg acgagactca ggaaattgat attatggaag gctatggcag tgatcggggg 420 ggaacttggt tcgcccaaag aatgcatttg agccaccata catttattcg taaccccttt 480 acggattatc agcctatggg agacgctaca tggtattaca acggaggtac accatggcgt 540 tcagcatatc accgttatgg atgttattgg aaagatccat ttacattgga atattatatt 600 gacggggtaa aggttagaac ggtcacaaga gccgaaattg atcctaataa tcatctcggc 660 ggaacagggt tgaatcaggc aacaaatatt attattgatt gtgaaaatca aacagattgg 720 aggcccgcgg ctactcaaga agaactggcc gatgatagca aaaatatctt ctgggtcgat 780 tggatacgtg tgtacaagcc tgttgcggta agtggaggtg gaaacaac 828 6 276 PRT Cytophaga drobachiensis 6 Ala Gln Asp Trp Asn Gly Ile Pro Val Pro Ala Asn Pro Gly Asn Gly 1 5 10 15 Met Thr Trp Gln Leu Gln Asp Asn Val Ser Asp Ser Phe Asn Tyr Thr 20 25 30 Ser Ser Glu Gly Asn Arg Pro Thr Ala Phe Thr Ser Lys Trp Lys Pro 35 40 45 Ser Tyr Ile Asn Gly Trp Thr Gly Pro Gly Ser Thr Ile Phe Asn Ala 50 55 60 Ala Gln Ala Trp Thr Asn Gly Ser Gln Leu Ala Ile Gln Ala Gln Pro 65 70 75 80 Ala Gly Asn Gly Lys Ser Tyr Asn Gly Ile Ile Thr Ser Lys Asn Lys 85 90 95 Ile Gln Tyr Pro Val Tyr Met Glu Ile Lys Ala Lys Ile Met Asp Gln 100 105 110 Val Leu Ala Asn Ala Phe Trp Thr Leu Thr Asp Asp Glu Thr Gln Glu 115 120 125 Ile Asp Ile Met Glu Gly Tyr Gly Ser Asp Arg Gly Gly Thr Trp Phe 130 135 140 Ala Gln Arg Met His Leu Ser His His Thr Phe Ile Arg Asn Pro Phe 145 150 155 160 Thr Asp Tyr Gln Pro Met Gly Asp Ala Thr Trp Tyr Tyr Asn Gly Gly 165 170 175 Thr Pro Trp Arg Ser Ala Tyr His Arg Tyr Gly Cys Tyr Trp Lys Asp 180 185 190 Pro Phe Thr Leu Glu Tyr Tyr Ile Asp Gly Val Lys Val Arg Thr Val 195 200 205 Thr Arg Ala Glu Ile Asp Pro Asn Asn His Leu Gly Gly Thr Gly Leu 210 215 220 Asn Gln Ala Thr Asn Ile Ile Ile Asp Cys Glu Asn Gln Thr Asp Trp 225 230 235 240 Arg Pro Ala Ala Thr Gln Glu Glu Leu Ala Asp Asp Ser Lys Asn Ile 245 250 255 Phe Trp Val Asp Trp Ile Arg Val Tyr Lys Pro Val Ala Val Ser Gly 260 265 270 Gly Gly Asn Asn 275 

What is claimed is:
 1. An isolated agaA gene coding for a β-agarase, characterized in that it has SEQ ID No.
 1. 2. An isolated agaB gene coding for a β-agarase, characterized in that it has SEQ ID No.
 3. 3. An isolated gene according to claim 1, characterized in that it codes for a β-agarase of Cytophaga drobachiensis deposited in the DSMZ Collection (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures)) on May 8, 1998 under the number DSM
 12170. 4. An isolated protein AgaA of the β-agarase type from C. drobachiensis DSM 12170, characterized in that it has SEQ ID No.
 2. 5. An isolated protein AgaB of the β-agarase type from C. drobachiensis DSM 12170, characterized in that it has SEQ ID No.
 4. 6. An isolated peptide fragment AgaA′ of the protein according to claim 4, characterized in that it has SEQ ID No. 6 and β-agarase activity.
 7. An isolated nucleic acid having a sequence coding for the protein according to claim
 4. 8. An isolated nucleic acid, characterized in that its sequence consists of: a) the DNA sequence SEQ ID No. 1 coding for the protein AgaA; b) a DNA sequence that, because of the degeneracy of the genetic code, is derived from sequence a) above and codes for the protein AgaA; or c) an mRNA sequence corresponding to a DNA sequence of a) or b) above.
 9. An isolated nucleic acid having a sequence coding for the protein according to claim
 5. 10. An isolated nucleic acid, characterized in that its sequence consists of: a) the DNA sequence SEQ ID No. 3 coding for the protein AgaB; b) a DNA sequence that, because of the degeneracy of the genetic code, is derived from sequence a) above and codes for the protein AgaB; or c) an mRNA sequence corresponding to a DNA sequence of a) or b) above.
 11. An isolated nucleic acid having a sequence coding for the peptide fragment according to claim
 6. 12. An isolated nucleic acid characterized in that its sequence consists of: a) the DNA sequence SEQ ID No. 5 coding for the peptide fragment AgaA′; b) a DNA sequence that, because of the degeneracy of the genetic code, is derived from sequence a) above and codes for the peptide fragment AgaA′; or c) an mRNA sequence corresponding to a DNA sequence of a) or b) above.
 13. Expression vector, characterized in that it comprises a nucleic acid sequence according to claim 7 and the means necessary for its expression.
 14. Host microorganisms or cells transformed by an expression vector according to claim
 13. 15. An isolated gene according to claim 2, characterized in that it codes for a β-agarase of Cytophaga drobachiensis deposited in the DSMZ Collection (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures)) on May 8, 1998 under the number DSM
 12170. 16. An expression vector, characterized in that it comprises a nucleic acid sequence according to claim 9 and the means necessary for its expression.
 17. A host microorganism or cell transformed by an expression vector according to claim
 16. 